Trajectory Frame Clustering Panel

Perform clustering on structures from a Desmond trajectory based on the RMSD matrix of a specified set of atoms.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Classical Simulation → Desmond Trajectory Clustering
  • Click the Tasks button and browse to Desmond → Desmond Trajectory Clustering
  • Click the Tasks button and browse to Biologics → Molecular Dynamics → Desmond Trajectory Clustering
  • Using
  • Features
  • Additional Resources

Trajectory Frame Clustering Panel

The trajectory to analyze must be specified via either an output CMS file for a Desmond or a project entry that incorporated the results of such a simulation. The frames used to calculate the RMSD for the clustering are selected from the trajectory at a specified interval, and by default the frames are superimposed before calculating the RMSD. The RMSD matrix is then used in the affinity propagation clustering method (Science 2007, 315, 972), with a specified maximum number of clusters. The results include a representative frame from each cluster.

The clustering job produces a CMS file for each cluster containing the representative structure for the cluster, and a log file.

Trajectory Frame Clustering Panel Features

Use structures from option menu

Choose the structure source for the current task. The structure specified must be a Desmond CMS file or one that is imported into the project.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
Open Project Table button

Open the Project Table panel, so you can select the entries for the structure source.

File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

RMSD Matrix section

Select the atoms to be used for the RMSD calculation and the frames that are clustered.

Use ASL buttons and text box

Provide an ASL (Atom Selection Language) expression for the atoms to use in the clustering of the frames. Click Select to open the Atom Selection dialog box to set up the ASL expression, or enter the expression in the text box. To clear the existing expression, click Clear.

Frequency text box

Specify the frequency N at which a frame is selected for an RMSD calculation. The RMSD is calculated for every Nth frame. The default is to calculate the RMSD for every 10th frame.

Clustering section

Set options for determining how many clusters to report.

Use up to N clusters text box

Set a limit on the number of clusters to generate. An output CMS file is written for each cluster.

Status display area

Displays status information on the clustering process.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

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